<<<<<<< HEAD ======= >>>>>>> ed2b44cf86718946e816938d7dab92b40f2517a7 Rui Fu’s CV

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Rui Fu

RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus

My research interests are in RNA degradation and post-transcriptional gene expression, interrogated through biochemical experiments and bioinformatic/computational analyses of genomic and sequencing data.

Education

Ph.D. Biological Science

University of California San Diego

La Jolla, CA, USA

2015 - 2009

B.S. Biological Science

Xiamen University

Xiamen, Fujian, China

2009 - 2005

Research Experience

Bioinformatic tool development:

clustifyr, automated single cell RNA-seq cell identity assignment Bioconductor package (author)

squirrelBox, RNA-seq data visualization, exploration, and analysis web browser built with R Shiny and JavaScript (author)

someta, quantification and monitoring of missing cell-level metadata in scRNA-seq GEO deposition (author)

scraps, scalable pipeline for extraction of polyadenylation site and sequencing internal priming information from scRNA-seq data (author)

valr, framework for tidyverse-style genomic interval analysis in R (co-developer)

Developed computational biology course materials:

  1. rnabioco.github.io/practical-data-analysis

  2. rnabioco.github.io/cellar

Semi-Independent Postdoctoral Informatics Fellow

Jay Hesselberth’s Supervision

University of Colorado Anschutz

Current - 2017

  • Development of bioinformatics software packages for single cell RNA sequencing
  • RNA post-transcriptional dynamics modeling of steroidogenesis
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  • RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain and liver
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  • RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain
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  • Collaboration on various single cell RNA sequencing projects
  • Analysis of human genetic variation from gnomAD database for insights into nonsense-mediated mRNA decay

Postdoctoral Research Fellow

Judy Lieberman’s Lab

Harvard Medical School

2017 - 2016

  • Identification of a mitochondrial trigger for apoptotic mRNA decay
  • Purification of cytotoxic granules and cytolytic proteins from NK cells
  • Mouse genetic manipulation by CRISPR-Cas9, and automated genotyping with custom R app

Graduate Research Assistant

Jens Lykke-Andersen’s Lab

University of California San Diego

2015 - 2009

  • Investigation of co-factors involved in ZFP36-mediated mRNA decay and translational repression during macrophage innate immune response
  • Characterization of the ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts

Undergraduate Research Assistant

Ruichuan Chen’s Lab

Xiamen University

2009 - 2007

  • Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
  • Mechanistic characterization of p-TEFb activation by HIV-Tat

Publications, as First or Corresp. Author

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells

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RNA

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Under review at RNA, preprint on bioRxiv

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N/A

2021

  • Fu R1, Wellman K1, Baldwin A, Rege J, Bartholomay K, Hirsekorn A, Riemondy K, Rainey W, Mukherjee N.

Cell-level metadata is indispensable for documenting single cell sequencing datasets

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PLOS Biology

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Revision at PLOS Biology, preprint on bioRxiv

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N/A

2021

  • Puntambekar S, Hesselberth J, Riemondy Kc, Fu Rc.

Liver transcriptome dynamics during hibernation are shaped by a shifting balance between transcription and RNA stability

Frontiers in Physiology

N/A

2021

  • Gillen A1, Fu R 1, Riemondy K1, Jager J, Fang B, Lazar M, Martin S.

Dynamic RNA regulation in the brain underlies physiological plasticity in a hibernating mammal

Frontiers in Physiology

N/A

2020

  • Fu R1, Gillen A1, Grabek K, Riemondy K, Epperson E, Bustamant C, Hesselberth J, Martin S.

clustifyr: an R package for automated single-cell RNA sequencing cluster classification

F1000Research

N/A

2020

  • Fu R, Gillen A, Sheridan R, Tian C, Daya M, Hao Y, Hesselberth J, Riemondy K.

PNPT1 release from mitochondria during apoptosis triggers decay of poly(A) RNAs

Cell

N/A

2018

  • Liu X1, Fu R1, Pan Y, Meza-Sosa K, Zhang Z, Lieberman J.

Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements

RNA

N/A

2016

  • Fu R, Olsen MT, Webb K, Bennett E, Lykke-Andersen J.

Publications, as Contributing Author

Microglial BTK Signaling Regulates Immune-Mediated Cortical Demyelination. In prep for Nature Medicine. Barr H, Given K, McClain C, Fu R, Gruber R, Ofengeim D, Macklin W, Bennett J, Owens G, Hughes E.

N/A

2021

Srsf3 mediates alternative RNA splicing downstream of PDGFRa signaling. Revision at Development, preprint on bioRxiv. Dennison B, Larson E, Fu R, Mo J, Fantauzzo K.

N/A

2021

Molecular tracking devices quantify antigen distribution and archiving in the lymph node. eLife. Walsh S, Sheridan R, Doan T, Lucas E, Ware B, Fu R, Burchill M, Hesselberth J, Tamburini B.

N/A

2021

Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases. European Respiratory Journal. Liao S, Shaikh A, Mould K, Konigsberg I, Fu R, Davidson E, Li L, Fontenot A, Maier L, Yang I.

N/A

2021

Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Acute Myeloid Leukemia Patients. Cancer Discovery. Pei S, Pollyea D, Gustafson A, Stevens B, Minhajuddin M, Fu R, Riemondy K, Gillen A, Sheridan R, Kim J, Costello J, Amaya M, Inguva A, Winters A, Ye H, Krug A, Jones C, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers J, Ashton J, Nemkov T, D’Alessandro A, Gutman J, Fesik S, Ramsey H, Savona M, Smith C, Jordan C.

N/A

2019

Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells. Frontiers in Immunology. Tamburini B, Finlon JM, Gillen A, Kriss M, Riemondy K, Fu R, Schuyler R, Hesselberth J, Rosen H, Burchill M.

N/A

2019

Single cell RNA Sequencing Identifies Transforming Growth Factor β as a Critical Regulator of Alveolar Regeneration. JCI Insight. Riemondy K, Jansing N, Jiang P, Redente E, Gillen A, Fu R, Anthony G, Hesselberth J, Zemans R.

N/A

2019

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. Nucleic Acid Research. Riemondy K, Ransom M, Alderman C, Gillen A, Fu R, Finlay-Schultz J, Kirkpatrick G, Di Paola J, Kabos P, Sartorius C, Hesselberth J.

N/A

2019

Posters and Talks

Interactive scRNA-seq cell-type classification via clustifyr identifies widespread omission of cell-level annotations in public data repositories. (Keystone eSymposia on Single Cell Biology - Poster, co-present with mentee)

N/A

2021

Towards a comprehensive view of dynamic RNA regulation in hibernating 13-lined ground squirrel. (EMBL Conference, From Functional Genomics to Systems Biology - Poster)

N/A

2020

ClustifyR: automated single-cell RNA sequencing cluster classification. (Keystone Symposia on Single Cell Biology - Poster)

N/A

2019

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis. (Boston Children’s Hospital PCMM Research Poster Session - Poster)

N/A

2017

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis. (Boston Children’s Hospital PCMM Research Poster Session - Poster)

N/A

2016

TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex. (Cold Spring Harbor Laboratory mRNA Processing Meeting - Presentation)

N/A

2015

TTP represses translation of target mRNAs through the 4EHP-GYF2 complex. (UCSD Mechanisms of Gene Expression Seminar - Presentation)

N/A

2014

TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition. (Cold Spring Harbor Laboratory mRNA Processing Meeting - Poster)

N/A

2013

The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression. (Keystone Symposia on Protein-RNA Interactions - Poster)

N/A

2012

Teaching Experience

Online Lecture Instructor (Graduate-Level Courses)

University of Colorado Anschutz

N/A

  • Informatics and Statistics for Molecular Biology (2020) - teaching and grading on RStudio Cloud platform
  • Foundations in Biomedical Sciences (2020) - online lecture, paper discussion, and homework/exam design on RNA biology
  • Workshop for scRNA-seq Data Analysis (2020) - course development and online lectures

Lecture Instructor (Graduate-Level Courses)

University of Colorado Anschutz

N/A

  • Rigor in Research (2020) - lecture on RNA sequencing
  • Foundations in Biomedical Sciences (2018, 2019) - lectures, paper discussion, and homework/exam design on RNA biology
  • Practical Data Analysis with R/RStudio (2018, 2019) - course development and lectures
  • Workshop for scRNA-seq Data Analysis (2019) - course development and lectures

Teaching Assistant (Graduate-Level Courses)

University of Colorado Anschutz

N/A

  • Practical Computational Biology for Biologists: R (2018, 2019)
  • Practical Computational Biology for Biologists: Python (2018, 2019)
  • Core Topics in Biomedical Sciences (2018)

Weekly RNA Bioscience Initiative Informatics Office Hour

University of Colorado Anschutz

N/A

  • Guidance on RNA and computational research questions from students and researchers of CU Anschutz Medical Campus

Teaching Assistant (Undergraduate-Level Courses)

University of California San Diego

N/A

  • Molecular Biology (2012)
  • DNA Recombination Lab (2011, 2012)

Mentoring Experience

RNA Bioscience Initiative Internship Mentoring

University of Colorado Anschutz

N/A

Current - 2020

  • Mentoring of undergraduate computer science student for 2020 summer internship and beyond
  • Project: systemic exploration of published scRNA-seq cell type signatures in the NCBI Gene Expression Omnibus
  • Mentee’s work was integrated into updates to R Bioconductor packages clustifyr and clustifyrdatahub, GitHub repo someta, first author communication/essay manuscript, and poster presentation.

Summer Research Mentoring

Harvard Medical School

N/A

2017

  • Mentoring of high school student enrolled in the MIT Research Science Institute program
  • Topics: tissue culture, RNA-related bench experiments, RNA-seq informatics analysis, and scientific writing

BS/MS Student Research Mentoring

University of California San Diego

N/A

2015 - 2013

  • Mentoring of student research spanning undergraduate honor thesis and master thesis on biochemical investigations of RNA-binding protein functions
  • Project: biochemical investigation of RNA-binding protein functions
  • Mentee’s work was integrated into second author 2016 RNA publication. Mentee was awarded Best Poster Presentation Award at 2014 UCSD Biological Sciences Annual Student Research Showcase.

Service and Training

Society memberships

RNA Society, International Society for Computational Biology, Genetics Society of America

N/A

Current - 2015

RNA Bioscience Initiative Grant Review

N/A

N/A

Current - 2019

GENETICS Early Career Reviewer (Cellular Genetics section)

4 manuscripts reviewed for GENETICS and G3, tinyurl.com/rev-rf

N/A

Current - 2018

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Organizer for CU Anschutz Immuno-Informatics Joint Journal Club

N/A

N/A

2020

Mentor Collective mentorship training

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Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project

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N/A

N/A

2019

Data Incubator Data Science Fellowship

N/A

N/A

2017

Grant writing training under Dr Lieberman

N/A

N/A

2016

Harvard Medical School Scientists Teaching Science Course

N/A

N/A

2016

Diversity, Equity, and Inclusion Service

RNA Society Volunteer - Writer for Scientist Spotlight

N/A

N/A

2021

CU Anschutz Medical Campus Equity Certificate Program training

N/A

N/A

2021

Admissions Committee for CU Graduate Experiences for Multicultural Students

N/A

N/A

2019

Mentor for CU Anschutz and Denver Campus ISCORE (undergraduate mentorship program)

N/A

N/A

2019

Recognition

Dr Huang Memorial Scholarship, UC San Diego

N/A

N/A

2011 - 2009

First-Class Scholarship

N/A

N/A

2008 - 2006

XMU University Merit Student

N/A

N/A

2008 - 2006

Science Outreach

Volunteer for CU Anschutz Medical Campus Young Hands in Science Outreach Program

tinyurl.com/younghandssci

N/A

2021

Facilitator at Denver Museum of Nature and Science - Prehistoric Journey section

N/A

N/A

2020 - 2019

Visitor Education Volunteer at the New England Aquarium

N/A

N/A

2017 - 2016

Information Ambassador at the San Diego Zoo

N/A

N/A

2016 - 2015

Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project

N/A

N/A

2012

Disclaimer

Made with pagedown.

Code at github.com/raysinensis/cv.

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Last updated on 2021-04-13.

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Last updated on 2021-03-16.

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